The major foundation of what has become Bowen University today was laid in 1854 by the family of the late Reverend Thomas Jefferson Bowen who started a school in Ijaiye Orile in the present Oyo State of Nigeria. The school, which comprised five stewards of the late Bowens, five other labourers, and a few others drawn to the fledging school by sheer curiosity, has grown from this little beginning into thousands of Baptist primary and secondary schools scattered across the country today. By 1960, there was a Baptist school almost everywhere a Baptist congregation exits.
The idea of establishing a Baptist University in Nigeria was first conceived in 1938. This was borne out of the Baptist commitment to assisting people to develop their potentials to the fullest. The first bold step towards actualizing this vision was taken in 1956 when a proposal was presented to the meeting of the Baptist Mission held in Eku from 11 to 14 December, 1956. On 16 and 17 July, 1957, the joint meeting of the Executive Committees of the Baptist Mission of Nigeria and the Nigerian Baptist Convention worked tirelessly, committing time, material and human resources to actualizing the vision.
Today, all these efforts have crystallized into the establishment of Bowen University, a significant landmark in the academic heritage of the Nigerian Baptist Convention, making it the first Baptist University in Africa.
On 17 July, 2001, the Federal Government of Nigeria approved the establishment of Bowen University and it was subsequently licensed to operate by the National Universities Commission. A Provisional Governing Council to manage the University was inaugurated on 22 August, 2001 with late Professor J.T. Okedara as the foundation Vice Chancellor, while Mr E. A. Lawale was appointed as the pioneer Registrar. Professor Okedara served as Vice Chancellor until July 2003. In August 2003, the incumbent Vice Chancellor, Professor Timothy Oyebade Olagbemiro, was appointed Vice Chancellor and is scheduled to complete a ten-year tenure of two terms in July 2013.